3N3Y

Crystal structure of Thymidylate Synthase X (ThyX) from Helicobacter pylori with FAD and dUMP at 2.31A resolution

PDB DOI: https://doi.org/10.2210/pdb3N3Y/pdb

Classification: TRANSFERASE
Organism(s): Helicobacter pylori SS1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-21 Released: 2011-05-25
Deposition Author(s): Wang, K., Wang, Q., Chen, J., Chen, L., Jiang, H., Shen, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.174 (Depositor), 0.170 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure, Enzymatic Characterization and Inhibitor Discovery of Thymidylate Synthase X (ThyX) from Helicobacter pylori Strain SS1

Wang, K., Wang, Q., Chen, J., Chen, L., Jiang, H., Shen, X.

To be published.

Macromolecule Content

Total Structure Weight: 104.17 kDa
Atom Count: 7,255
Modelled Residue Count: 834
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase thyX	A, B, C, D	216	Helicobacter pylori SS1	Mutation(s): 0 Gene Names: ThyX EC: 2.1.1.148
UniProt
Find proteins for Q5UVJ4 (Helicobacter pylori) Explore Q5UVJ4 Go to UniProtKB: Q5UVJ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5UVJ4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth D] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	F [auth A], I [auth B], K [auth C], M [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
UMP Query on UMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], H [auth B], J [auth C], L [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.174 (Depositor), 0.170 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.525	α = 90
b = 79.956	β = 103.14
c = 96.405	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-05-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations